LTER CTD Instrument Workup 2019
Christina Bonsell
Oct 4, 2019
Temperature and Salinity Workup from raw data:
- Compare datalogger data to each other and to YSI sonde data
- Present some background summaries and visualizations comparing instruments
- Choose datasets best representative of station hydrography, default to RBR
- Flag “invalid” data via algorithm based on freezing line
- Calibrate EWLD1 and KALD1 (StarOddi) using YSI data
- Show some comparison plots b/n calibrated and uncalibrated data
- Manually add “Qustionable measurement” flags to questionable conductivity/salinity data and EELD1temerature data form when it was in mud
- Write derived (calibrated, QA/QCd) dataset
CTD-QAQC.Rmd is a cleaned-up version that just returns derived datasets and final plots
Import CTD data
First few rows:
## # A tibble: 6 x 12
## Station DT Conductivity Temperature Pressure
## <chr> <dttm> <dbl> <dbl> <dbl>
## 1 EWLD2 2018-08-11 17:00:00 29.2 5.46 13.6
## 2 EWLD2 2018-08-11 18:00:00 29.2 5.47 13.5
## 3 EWLD2 2018-08-11 19:00:00 29.2 5.47 13.5
## 4 EWLD2 2018-08-11 20:00:00 29.2 5.46 13.5
## 5 EWLD2 2018-08-11 21:00:00 29.2 5.44 13.5
## 6 EWLD2 2018-08-11 22:00:00 29.1 5.42 13.5
## # ... with 7 more variables: `Sea pressure` <dbl>, Depth <dbl>,
## # Salinity <dbl>, `Speed of sound` <dbl>, `Specific conductivity` <dbl>,
## # `Density anomaly` <dbl>, Instrument <chr>## # A tibble: 6 x 9
## Station Date Time Temp_C Sal Cond_mspercm SoundVel_mpers
## <chr> <chr> <tim> <dbl> <dbl> <dbl> <dbl>
## 1 KALD1 07.0~ 16:00 5.51 32.8 32 1470.
## 2 KALD1 07.0~ 17:00 5.22 33.4 32.3 1469.
## 3 KALD1 07.0~ 18:00 5.15 32.7 31.6 1468.
## 4 KALD1 07.0~ 19:00 5 24.5 24.2 1457.
## 5 KALD1 07.0~ 20:00 4.93 17.6 17.8 1448.
## 6 KALD1 07.0~ 21:00 4.74 16.8 17.0 1446.
## # ... with 2 more variables: DT <dttm>, Instrument <chr>## # A tibble: 6 x 5
## FileName `ISO 8601 Time` `Temperature (C~ Station Instrument
## <chr> <dttm> <dbl> <chr> <chr>
## 1 ./data/1805214_1~ 2018-08-07 17:00:00 5.61 KALD1 TCM
## 2 ./data/1805214_1~ 2018-08-07 18:00:00 5.42 KALD1 TCM
## 3 ./data/1805214_1~ 2018-08-07 19:00:00 5.28 KALD1 TCM
## 4 ./data/1805214_1~ 2018-08-07 20:00:00 5.05 KALD1 TCM
## 5 ./data/1805214_1~ 2018-08-07 21:00:00 5.03 KALD1 TCM
## 6 ./data/1805214_1~ 2018-08-07 22:00:00 5.08 KALD1 TCMImport YSI data
First few rows:
## # A tibble: 6 x 5
## Station DT Salinity Temperature Conductivity
## <chr> <dttm> <dbl> <dbl> <dbl>
## 1 EELD1 2019-04-16 12:00:00 35.3 -1.8 27.8
## 2 EELD1 2019-07-31 20:00:00 24.6 9.1 26.9
## 3 EELD2 2019-07-31 18:00:00 25.9 7.7 27.3
## 4 EWLD1 2018-08-11 18:00:00 27.3 6.8 43.0
## 5 EWLD1 2019-04-13 19:00:00 34.6 -2 27.2
## 6 EWLD1 2019-06-23 18:00:00 10.5 -0.3 9.59Compare instrument types (color points) to YSI data (black points)
EWLD1 and KALD1 could use calibration
in April in Jago (JAL), high amounts of stratification meant that YSI may not have hit correct depth and cond/sal reading may be off
Difference in readings between instruments
Calibrate EWLD1 and KALD1 using YSI data
T vs S to check for erroneous data via freezing line
What to flag (“anom” data is below TS line givin instrument precision)
## [1] "SO error: T=0.1, Cond=1.5 mS/cm, RBR error: T=0.002, Cond=0.01 mS/cm"
Choose datasets to use in final table
color=StarOddi, black=RBR
use KALD1 calibrated for Temp and Cond, EWLD1 calibrated for Cond
Next step = Flagging data
Values below freezing line (with error) are flagged “INV” for Invalid
Values that are outliers, or appear to be instrument malfunction (as determined by a trained human), or are from when instrument was in mud (EELD1 RBR pulled up coated in mud, attached to negatively buoyant SeaFET) are flagged “QM” for Questionable Measurement
Finalize tables and display data
